Stéphane,
I'm willing to do some FEP using the slow groth approach available in gromacs (as of 3.3.1). While retrieving articles and the mailing list, i found out there where arguments against sequential runs (particularly for avoiding the hysteresis problem), and other against parallel runs.
If you are doing slow growth, that is an entirely different thing from doing parallel or sequential lambda runs. Slow growth gradually changes lambda from 0 to 1 in a continuous manner over the course of a simulation and I don't recommend it unless you have a particular problem where this is the only way to do it or something. But generally it leads to Hamiltonian lag.
I would greatly appreciate your opinion about running a parallel (double precision) or sequential procedure (with 20 lambdas for 200ps of equilibration and 300 ps of 'production' for each lambda), and if possible some pointers towards documentation (i've read the manual, the Dill's group tutorial, the chapter from Leach, and some other publication from Aqvist, but still i'm not completely convinced of the procedure).
I need to write a tutorial for this sort of thing, but it is still in the works. Can you be more specific about what exactly you're confused about? I would DEFINITELY run parallel. If you run sequentially, there are three or four big disadvantages: (1) What happens at each lambda is coupled to what happened at the one before. (2) There can be hysteresis (partly as a result of 1), which is bad. (3) You can't benefit from the 'trivial parallelization' offered by running independently at multiple lambda values, which usually will mean you will run shorter simulations. That is, suppose you have 20 lambda values, and you would want to run 1 ns for each. Now, you have to run one 20 ns simulation if you do them in serial, or 20 1 ns simulations if you run them in parallel. Unless you have only one computer, you usually will finish your project a lot faster if you go with the second option. (4) If you decide you need to simulate longer at one particular lambda value (say, lambda=0.5), you then need to re-run ALL of the simulations you ran after that one (i.e. lambda=0.5->1.0, if you're moving to the right). In terms of implementation, what I do is I prepare a particular equiliibrated structure of my system in water. Then I set up run input files for all of my different lambda values, and I then minimize and equilibrate my system AGAIN at each different lambda value, so now I have nlambda different equilibrated structures, each appropriate for a different lambda value. I then run production beginning with each of these structures. I generally do 1 ns of equilibration of my system as a whole initially, then re-equilibrate at each lambda value for another 100ps+. But these numbers will vary depending on what you're studying. If your system equilibrates only very slowly, you may need to equilibrate a lot longer. After equilibration, I run at least 1 ns of production at each lambda value. Again, this will depend on your system and what you can computationally afford. Best wishes, David
Yours, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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